1. Welcome to the Maps and CMap Tutorial
Identify the location of a particular gene, trait, QTL or marker - and the grass species they have been mapped to - on genetic, QTL, physical, sequence, and deletion maps .
Use the CMap viewer to examine the co-linearity of a particular region in one chromosome or species to another; or infer which linkage group in one species is most conserved with a linkage group in another species. .
Determine which maps are the best for making comparisons.
v.26
Welcome to the Maps and CMap Tutorial
Listed are some of the things you can do while in the Maps module.
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2. For more assistance on cmap, visit http://www.gmod.org/cmap/
GMOD
CMap was originally written for the Gramene project ( and is now part of the GMOD (Generic Model Organism Database) Project (
For more assistance on cmap, visit
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3. Tutorial Tips
If you are viewing this tutorial with Adobe Acrobat Reader, click the "bookmarks" on the left hand side of the Reader for easier navigation.
Note! Although we continually work to make Gramene compatible with all browsers, there are problems with some browser versions. If you're having difficulty viewing Gramene, try using a different browser. Please report any problems with browsers through Gramene Feedback.
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4. Click here to open the Maps Home Page
Gramene Home Page
Click here to open the Maps Home Page
On the Gramene Home Page ( click on “Maps” on the upper Gramene Navigation Bar to open the Maps Home Page.
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5. Concepts
Related maps are grouped into map sets. Generally, these are the result of a particular study, such as the set of linkage groups produced by a genetic mapping study.
A map is a linear array of interconnected features. This could represent a single linkage group in the case of a genetic map, or a single contig for physical maps.
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6. Concepts, con’t.
Any item that is positioned on a map is called a feature. The position may be either a point or an interval. Different feature types are represented by different shapes or colors.
The lines that connect features on one map to features on another map denote correspondences. These correspondences are assigned either automatically (based on feature name) or manually by the data curator to designate features on different maps that are equivalent in some manner. Different colors represent different correspondence types.
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7. Concepts, con’t.
The data in Maps has been imported from the Gramene Markers DB. Use maps to find a feature on a map, but use the Markers DB to get specific data about the features and map sets.
Not all the data in the Markers DB has been exported to CMap, only data that has correspondences has been imported into Maps. Some data, such as the OMAP stacked maps will be found only in Maps, and not in Markers.
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8. Module Home-Page layout
Module home pages provide the following information:
Searching/Browsing – links to different types of searches.
Other Tools – if applicable, links to different tools used in this module.
Help – links to help pages, tutorials, release notes, FAQ and other helpful documentation.
Download – information on where to download the database.
Feedback – How to contact Gramene
Acknowledgements – Other programs that contribute to this data.
Quicklinks and external links – when appropriate these links are provided.
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9. Maps Home Page
Select “maps” to choose a starting map. You may later add comparative maps to the right or left.
In Maps, a map is a linear array of interconnected features. This could represent a single linkage group in the case of a genetic map, or a single contig for physical maps. Related maps are grouped into map sets. Generally, these are the result of a particular study, such as the set of linkage groups produced by a genetic mapping study. For more information about the map sets contained in the database, visit the Map Set Info page.
The Maps home page (formerly known as CMap) can seem a bit overwhelming to the new user. Going through this tutorial should help you to identify the possible queries in the maps database. To begin exploring the maps, click on “maps” from the map menu.
Access OMAP data (see slide 28)
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10. 1. Select a species and click “Change Species”.
Maps: Select a Species
1. Select a species and click “Change Species”.
In Maps, you can use the CMap tool to compare maps. (For more information on CMap see To set up a comparison, a user first selects a reference map set, then a reference map from that map set. This serves as the basis for any comparisons that the user chooses to make. Once the reference map image has been rendered, the user is given the option to select one or two comparative maps. These comparative maps may be added to both the left and the right of the reference map. The user may keep adding additional maps for as long as valid comparisons are available.
Begin by selecting your reference map, to which other maps can be compared. First, select which species you would like maps for, and then click on the “change species” button to submit your request.. Only map sets from this species will be displayed in the next drop-down list. Note that selecting a new reference species will reset all other map options. .
You need to use the “reference menu” to select a species, map set and map that you will be able to compare other maps to later
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11. Maps: Select a Map Set
Click here for more information on map sets (see slide 40).
Map type, species, and name are shown
2. Select a reference map set, and click “Show Selected Set’s Maps”
Second, select a reference map set from the drop-down list, which is restricted based upon the species chosen. For descriptions of all the map sets, see the Map Set page. You must select a reference map set before any of the other options become available. Selecting a new reference map set at any time will reset all other map options. Note on the bottom of the next slide that the reference map set info will be displayed.
Reference Set Options will depend upon the reference species you have chosen. They are grouped by map types (sequence, genetic, etc). Displayed names may differ be abbreviated differently in different releases.
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12. Information on the Ref. Map Set will appear when one is selected.
Maps: Select a Map
3a. Choose one or all of the maps from this set (use ctrl to make multiple selections).
d. Click “Draw Maps”
b. If you have selected only one map from the mapset, you may select area to view by entering coordinates, if known.
c. Select options. The "Other" value refers to feature types that are not on the current maps but may be on comparative maps.
Select a reference map from the drop-down list. The list is limited to maps that are part of the selected map set. You must first select a reference map set before this option becomes available. Choosing a reference map allows other options to become available.
Any item that is positioned on a map is called a feature. The position may be either a point or an interval.
If only one map is selected from the reference maps list, a start and stop can be specified for the map.
Select how each feature types will be handled. Choose to ignore, display or display only those features that have correspondences displayed. The "Other" value tells Maps how to handle feature types that are not on the current maps but may be on comparative maps.
After selecting a reference map set, you will notice that the “Reference Map Set Info” will provide you with more information about the selected map set If it is the appropriate map set, select a reference map (identified by chromosome number) from the drop-down list. The list is limited to maps that are part of the selected map set. Choosing a reference map allows other options to become available.
Information on the Ref. Map Set will appear when one is selected.
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13. Maps: Viewing a map
Hover over a point for name and position, click for feature detail (see slide 14)
Click arrow to crop map (as in slide 23)
Change Magnification
Once a user has selected a reference map set and a reference map, it is immediately rendered as a map image. By default, the entire length of the map is displayed. At the top of the image is a box in which is printed the species, map set name, and map name as well as a combination of the controls as explained in the legend (see slide 12)
A vertical scale bar indicates positions along the length of the map. The distance measure (e.g., cM) being used is printed at the bottom of the scale bar. Features are drawn at appropriate positions. A legend for the various feature types shown on the map is printed at the bottom of the image. Click on a feature label to view the feature details page for that feature.
Note that not every feature may be labeled. The drawing algorithm will try to fit as many labels as it can, until there is no more available space. To see more labels, you may wish to increase the image size or decrease the font size. You may also specify "Start" and "End" positions to zoom in to a particular region on the reference map.
If two or more maps are being compared, each map will be drawn in a separate regions. Adjacent maps will have correspondence lines that connect corresponding features. The color of the line depends on the type of correspondence, indicated in the legend at the bottom of the map image.
In the lower-right-hand corner is a watermark indicating the version of CMap used to draw the map. This is also hyperlinked to the CMap homepage,
Scroll page for Map options – see slides 16-21
Map Legend (see slide 30)
Bookmarks for this page will fail after this session expires. Use the "Save Link" button to create a permanent link (see slide 45)
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14. Viewing a Map - Feature Detail
Click here for Map Details (see slide 15), as well as other information.
Link to QTL information (See QTL tutorial)
This page displays a feature’s accession ID, type, name, any aliases, its map and location as well as any applicable attributes or cross-references assigned by the curator. In addition, all the correspondences are displayed in a table.
The feature details page lists what is known about a feature and its correspondences. Details include: Unique accession ID, feature type and name. Synonyms, aliases, or other names by which a feature may be known, the map on which this feature may be found, (click on "View on Map" to see the map with the feature highlighted), the start and stop positions (no entry ("NULL") means that the feature is a point), links to external databases or additional attributes the curator has defined. At the bottom the correspondences table lists all the corresponding features from other maps associated with the feature. Click on the feature's name to view the feature details page for the corresponding feature. "View On Map" takes you to the appropriate map with the corresponding feature highlighted. "Comparative View" also takes you to the Map Viewer, but with both the original reference map and the corresponding map being compared.
Different features may offer different information and links to detail or map pages.
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15. Map Detail Note: “Map Details” will appear at the bottom of the page
When clicking “Map Detail” from previous slide you now get a map with your features highlighted.
Below the map and map options is your map Detail.
Map features presents a list of all features on this map.
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Map Legend, see slide 30

16. Update to show 3 more buttons
Options
Update to show 3 more buttons
Below the map are options menus. (Slides 17-22)
Click [+] to open the menus
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17. Defaults are to display entire chromosome at original magnification
Defaults are to display entire chromosome at original magnification. You may customize these.
Map Options
Use to compare maps, click the side (s) you wish to place them on. (see slide 24 and associated slides)
If multiple maps are displayed, this option displays them from top to bottom rather than left to right
Click to display map upside down from default view
Click to view another map or begin a new comparison
Click to collapse (hide) map options.
Click to add changes.
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18. Type in a feature name to highlight it on the map (as in slide 14).
All Labels
Feature Options
Type in a feature name to highlight it on the map (as in slide 14).
Determine which feature types to include on the maps, and when to display them, by selecting the appropriate boxes.
Determines which feature labels will be shown on the map. Landmarks are not currently active at Gramene.
Determines whether to use one or multiple glyphs for features that span over the same coordinates. “yes” is recommended
Click to add changes.
Click to collapse (hide) feature options.
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Features not overlapped

19. Correspondence Options
The “Correspondence Type” field allows restriction of correspondences by evidence type.
Each Map set displayed on the image is represented in this table. The individual maps are also displayed unless there are a large number in the slot. The reference map set is shaded a different color.
Add Maps Left/Right
Opens up the comparison menu (see below).
Min. Correspondences
This option is available for each of the comparison map sets. Indicate an integer value of the minimum number of correspondences that a map must have to another map in order to be displayed.
Stack Vertically
This option is available only for the reference set. If there are multiple reference maps, you can choose to have them side by side or stacked vertically.
Start/Stop
Each individual map has this option. It dictates the start and stop can be specified for the map.
Magnification
Each individual map has this option. It dictates the magnification of this map compared to it's original size.
Flip
Each individual map has this option. It dictates if this map is flipped.
Click to add changes.
Click to collapse (hide) correspondence options.
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20. Display Options Determines the vertical height of the image
Determines the size of the font
Select the desired image format.
Click to collapse (hide) display options.
Click to add changes.
Below the maps you will find places to change your viewable options. Underneath “Additional Options” you may:
Select the desired size of the image, size of the fonts, image format, labels (Show no labels; Show labels of features designated as landmarks or correspondences; or Show all labels that will fit in the image), collapse overlapping features (collapse spanning features of the same type which occupy the exact same coordinates as other features).
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21. Advanced Options
Predefined Order: Maps are ordered in the selection menu based on that specified in the database
Number of Correspondences: Maps are ordered based on the number of correspondences with the reference map
Click to collapse (hide) advanced options.
If “No” maps are drawn according to their specified length – If “Yes” maps are drawn to the same length
Having too many clickable features may be problematic for some browsers. If the number of features to be displayed is too large during a sanity check, features will not be clickable in order to prevent these problems.
Other: Everything is clickable
Omit Features: Features and feature labels are not clickable. Speeds up image display.
Omit All Buttons: The little menu buttons on the image (e.g., [i], [?], [M]) are also removed as well as the crop arrows and magnification controls. Use this to generate a final image for publication.
Click to add changes.
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22. The Same Maps: Displaying Different Options
The two images here reflect the same map comparison with different options selected for display.
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23. Click arrow to zoom in onto section it is pointing to.
Zooming/Cropping
Zooming in on a map displays only a part of the entire maps and allows more features to be seen
At the ends of the chromosome, the arrow indicates the chromosome continues, a solid bar indicates the end point
Click arrow to zoom in onto section it is pointing to.
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24. Compare Maps You may use the CMap viewer to compare maps.
Start with a reference map, which will serve as the basis for any comparisons. (Often this is a well documented map.)
Then select one or two comparative maps. These comparative maps may be added to both the left and the right of the reference map.
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25. For simplicity we will use our currently loaded QTL map
Select reference map
For simplicity we will use our currently loaded QTL map
But. sequence maps are well documented and therefore are a good reference map for comparisons, so it is a good idea to start with a sequence map as the reference map when making multiple map comparisons
Cropping your reference map to the area of interest will limit the possible comparison maps to only those with correspondences to your area of interest.
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26. Select comparative maps
See slide 17 to see how to open comparative maps displays.
The number in brackets for the mapset indicates the number of corresponding maps
Select comparative maps
The number in brackets for a map indicates the number of correspondences to the reference map.
You may determine the minimum number of correspondences that are desired from map to map.
Select a map or maps to compare with your reference map, and click “Redraw” or “Add Maps”
You may place maps for comparison on the left and right of the reference map (and continuing on, ad infinitum).
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27. Comparative Map Viewer
Lines show correspondences. The color of the line denotes evidence type (noted in legend). When multiple evidences support a correspondence, the one with the highest rank is used to color the line (see slide 43 for rankings).
Use the legend to help you interpret the maps. Correspondences will be indicated by lines, the color of which will depend upon the type of evidence.
Crop to zoom in to your areas of interest.
Features with correspondences appear in red (noted in legend)
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28. OMAP
The OMAP FPC maps are now available as ordered maps. These ordered maps offer faster rendering and a more compact arrangement, where contigs are displayed as a single map rather than as individual entities. The order of contigs on these ordered maps is based on correspondences to a reference map, namely the rice TIGR genome assembly. The user may view contig and clone mappings based on BAC end sequence alignments across a given chromosome.
See slide 4 for access to wild rice (Oryza sp) data.
A view showing the contig to contig mapping from the O. nivara ordered map to the TIGR genome assembly
Using Features options, select “stacked FPC contigs” and “FPC”
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29. We can layer in clone mappings in the ordered map to show structural rearrangements between maps. In this example, we see a large scale inversion between O. nivara and O. sativa. This is shown using evidence from the clone mapping in the ordered O. nivara FPContig as compared to the O. sativa TIGR V4 assembly.
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30. Map Legend Species name Map set name Map name
Legend at bottom of map explains options above. click on them to affect the display as described in the legend.
Listing of all the feature types found on the map, along with their corresponding glyphs
[i] Map set info –(slide 40)
[?] Map details (slide 14)
[M] Matrix View – (slide 36)
[L] Limit to one map – displayed when there is more than one map in the panel, select a single map by selecting [L] for the desired map.
[X] delete the map or mapset this symbol is associated with.
[F] Flip map – good for when most correspondences cross over each other.
[UF] Unflip map – displayed only when a map is flipped.
[N] New map view – limit the display to only this map.
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31. Maps: Legend - Glyphs
The following demonstrate some of the glyphs (shapes) that map features could appear as.
line
span
dumbbell
box
in-triangle
filled-box
out-triangle
Maps will use different glyphs and colors for different features.
up-arrow
down-arrow
double-arrow
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32. Map Search Search maps in CMap by species.
Map Search Help
The Map Search page allows a user to search for particular features maps or maps based on the map name or the number of related maps. Names" box, separating them with whitespace or commas.
Map sets available depend upon the species you selected.
Name must match name in database, so it may be easier to leave this blank unless you know the exact name (Chr. 1).
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33. Map Search Results
The results give you information about the maps in matrix form. This information is sortable by hyperlinked column headings.
The results give you information about the maps, such as the number of each feature type on the map. This information is sortable.
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34. 2. Choose a species (optional)
Search for a particular feature by name or accession ID, species, and feature type.
Feature Search
2. Choose a species (optional)
4. Search either the feature’s name (and aliases) or accession ID
Simply type in one or more names in the "Feature Names" box, separating them with white space or commas; if the feature you are searching for has spaces in the name, then enclose the feature name in double quotes. You can use "*" or "%" as wildcards. By default, both the feature name and alternate name fields will be searched, but this may be restricted to one or the other. You can filter the results by species and by feature type.
3. Choose a feature type (optional)
1. Type the feature name(s) you wish to search for in CMap. Wildcards allow you to search partial names.
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5. Click “Submit”

35. Feature Search Results
Found 61 features with a name or alias containing “YLD” in the species “Pearl Millet.”
Select to view the “Feature Details” Page for this feature (see slide 14)
Click on a hyperlinked column title to sort list by that column.
Click on any of the hyperlinked column headers will resort the search by that column.
If too many results are returned, then you will see several pages of results. You can navigate the results using the "Previous" and "Next" links or by providing on a specific page number.
For each name found, all the maps on which they occur will be displayed. Clicking on "View On Map" will take you to the map details page with the appropriate feature highlighted, and the "Feature Details" link will take you directly to the detailed information on the feature.
Select to view the “Map Set Info” (see slide 40)
Select to view this feature highlighted on a map (as in slide 15)
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36. Correspondence Matrix
Select to view the number of correspondences among all maps and choose a pair to display
In its initial view, the matrix shows the number of correspondences between pairs of map sets. Click on a number in a cell to view a more detailed comparison between a pair of map sets, broken down by map. In this detailed view, clicking on a number in a cell will bring you the map viewer showing a comparison of the two maps. The matrix is a cross-tabulated table showing the number of correspondences among all the map sets. When you first visit the matrix, you will be prompted to restrict the reference maps (the rows) by map type and/or species as the table can be quite large.
Options
Similarly to comparing maps begin by selecting a reference set by type and species.
Click “Submit”
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37. Multiple Mapset Matrix
The rest of the mapsets are those that have correspondences to the reference maps.
These are the available maps from your map type and species (Rice QTL)
Continue to select from choices, or…
Simply click on the number of correspondences between the mapsets to view the matrix.
These two mapsets have 289 correspondences among 19 maps
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38. Two-MapSet Matrix
In this example, we have narrowed it down to two mapsets – the QTL mapset as the reference, and a Sequence mapset as the comparison.
Clicking on a number in a cell will take you to the Map Viewer showing the comparisons of the two corresponding maps (see next slide).
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39. Comparing 2 maps
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40. Map Sets There are207 map sets.
Choose a species and/or a map type to filter your search.
This page contains information on all the map sets, including their species, map type, names (“short” and “long”), any additional attributes the curator has assigned (e.g., “Description”), the names of the maps in the set (for non-relational maps) with links to view those maps (or “all”) in the viewer, and the feature types occurring on the maps in the set. There can be many map sets on the page, so you can restrict the sets with the controls at the top of the page.
Follow links for more information.
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41. Feature Type Select a single feature There are 25 feature types
These are the feature types used in Cmap – only features that have correlations to other features will be here.. Each feature type has a name, a color and a shape. The curator may additionally assign other attributes (such as a “Description”) and cross-references.
This page displays each feature type's name, shape, color and description.
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42. These are the map types used to classify the maps
These are the map types used to classify the maps. Listed are the map type name & accession ID, the map units, an indication as to whether maps of this type are “relational,” and an indication of how maps of this are normally drawn (though this can be overridden at the map set level).
Map Type
This page displays each map type's map units, shape, width, and color. Additionally, each map type is flagged as to whether or not it is considered by the curators as a "relational only" map, meaning that maps of this type can only be viewed in relation to some reference map.
You may click to view all map sets of this map type
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43. Correspondence Evidence Types
These define the evidence types used to support the correspondences. Each evidence has an accession ID, a rank relative to the other evidence types, and an assigned color for the line drawn on the map to differentiate the correspondence.
This page lists the name an evidence type, its accession ID, rank (in relation to other evidence types), the color of the line representing the correspondence, and any attributes or cross-references established by the curators.
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44. Species Gramene currently has maps for 28 species.
List of mapsets may be filtered by individual species.
Species’ common and full names along with any other attributes and cross-references the curators have created.
Gramene has over 100 mapsets for rice.
Follow links for map information
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45. Saved Links
When someone creates a saved link (see slide 12) you can retrieve it here.
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46. Maps Help
Maps Menu
When clicking on Help from the maps menu, you will be directed to the help page for the section of the Maps module that you were viewing.
Maps Help Menu
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47. Tutorial Tutorials are available in various formats.
Link to any of the Gramene tutorials.
Download software for viewing tutorials.
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48. FAQ Search FAQ Use Feedback to ask a question
Click on a question or FAQ section to open and close the information..
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49. Email Gramene at gramene@gramene.org
Contact Gramene
Use the feedback button, located at the top of every page, to provide feedback or to ask questions about Gramene. or
Gramene at
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